Phenological variation associates with the stability of fruit quality traits in cultivated tetraploid blueberry

Fruit quality represents the major constraints to consumer acceptance of new blueberry cultivars. However, breeding for fruit quality is challenging due to its complex inheritance and genotype × environment interaction. Despite previous efforts to detect quantitative trait loci (QTL) associated with fruit quality traits, most of the identified QTL explain only a fraction of the total variability or lack stability across multiple environments. In this study, we investigated multiple fruit quality traits and phenology-related traits of 187 diverse southern highbush blueberry germplasm over 2-4 years. Significant phenotypic variation across observation years was detected for most traits. Genome-wide association study (GWAS) failed to identify stable peaks supported by multiple observation years, indicating complex control of fruit-related traits. To elucidate factors contributing to phenotypic variation, the relationship between observed phenotypic values and the stability measure of these values was examined. Significant correlations were found between the variation of phenology-related traits and the stability of fruit-related traits; it was found that early blooming and ripening accessions tended to exhibit variable firmness over the years. Additionally, size variability was influenced by the fruit size itself: accessions producing smaller fruit tended to show more variation in size over the years. Furthermore, GWAS conducted on the stability indices identified novel marker-trait associations that were not detected using normalized phenotypic values only, and their effects on fruit-related traits were similarly dependent on environment (observation year). Collectively, these findings deepen our understanding of variability in fruit-related traits and provide insights into their genetic control, thereby advancing breeding for superior cultivars with stable phenotypic performance.